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Liu W, Zhu C, Gao S, Ma K, Zhang S, Du Q, Sui K, Liu C, Chi Z. A biosensor encompassing fusarinine C-magnetic nanoparticles and aptamer-red/green carbon dots for dual-channel fluorescent and RGB discrimination of Campylobacter and Aliarcobacter. Talanta 2024; 266:125085. [PMID: 37619471 DOI: 10.1016/j.talanta.2023.125085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/29/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
The diarrhea pathogens Campylobacter and Aliarcobacter are similar in morphology and their leading symptoms, making them difficult to be differentially diagnosed. Herein, we report a biosensor with two modules to differentiate the genera-representative species of C. jejuni and A. butzleri. Module 1 was fusarinine C-decorated magnetic nanoparticles; module 2 consisted of C. jejuni-specific aptamer modified with red-emitting carbon dots (CDs) and A. butzleri-specific aptamer-modified green-emitting CDs, consisting non-interfering dual-fluorescence detection channels. Module 1 was used to selectively capture C. jejuni and A. butzleri from an un-cultured sample, and the specific CDs in module 2 would then recognize and bind to their counterpart bacteria when subjected to the collected module 1-bacteria complex. By measuring the fluorescence intensities from the CDs-bound bacteria, the abundance of each bacterium could be differentially indicated. This biosensor exhibited a wide detection range of up to 1 × 107 CFU/mL and the lowest limit of detection (LOD) of 1 CFU/mL, for each bacterium. Thus, the biosensor with dual-fluorescent channels facilitated a culture-independent, ultrasensitive and discriminative detection of C. jejuni and A. butzleri. Remarkably, this fluorescent detection could be transformed into RGB color indication to render the visual discrimination. After the biosensor was coupled with microfluidics, a biosensing platform was developed, which could render fluorescent and RGB differentiation of the two bacteria in human stool or chicken broilers, achieving a LOD of 5 CFU/mL and turnaround time of 65 min. This work established the first biosensor-based methodology for the discriminative detection of Campylobacter and Aliarcobacter in real samples.
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Affiliation(s)
- Weixing Liu
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, 266003, Qingdao, China
| | - Chengrui Zhu
- Haide College, Ocean University of China, No. 238 Songling Road, 266100, Qingdao, China
| | - Shaoqian Gao
- Haide College, Ocean University of China, No. 238 Songling Road, 266100, Qingdao, China
| | - Keran Ma
- Haide College, Ocean University of China, No. 238 Songling Road, 266100, Qingdao, China
| | - Shangxian Zhang
- Haide College, Ocean University of China, No. 238 Songling Road, 266100, Qingdao, China
| | - Qingbao Du
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, 266003, Qingdao, China; Qingdao Sinova-HK Biotechnology Co., Ltd, No. 5138 Haixi Middle Road, 266423, Qingdao, China
| | - Kangmin Sui
- Qingdao Municipal Hospital, University of Health and Rehabilitation Science, No. 5 Donghai Middle Road, 266071, Qingdao, China.
| | - Chenguang Liu
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, 266003, Qingdao, China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, 266003, Qingdao, China.
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Iwata T, Kurahashi Y, Wijaya IMM, Kandori H. Spectroscopic Investigation of Na +-Dependent Conformational Changes of a Cyclobutane Pyrimidine Dimer-Repairing Deoxyribozyme. ACS OMEGA 2023; 8:37274-37281. [PMID: 37841180 PMCID: PMC10569015 DOI: 10.1021/acsomega.3c05083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/19/2023] [Indexed: 10/17/2023]
Abstract
UV1C is an enzymatically active DNA sequence (deoxyribozyme, DNAzyme) that functions as a cyclobutane pyrimidine dimer (CPD) photolyase. UV1C forms parallel guanine quadruplexes (G-quadruplexes) with a DNA substrate in the presence of 240 mM Na+, the structure of which is important for the enzymatic activity. To investigate the repair mechanism of CPD by UV1C, we designed light-induced Fourier transform infrared (FTIR) spectroscopy. Prior to FTIR measurements, circular dichroism (CD) spectroscopy was conducted to determine the Na+ concentration at which the most G-quadruplexes were formed. We found that UV1C also forms a hybrid G-quadruplex structure at over 500 mM Na+. By assuming a concentration equilibrium between G-quadruplexes and Na+, 1.3 and 1.8 Na+ were found to bind to parallel and hybrid G-quadruplexes, respectively. The hybrid G-quadruplex form of UV1C was also suggested to exhibit photolyase activity. Light-induced FTIR spectra recorded upon the photorepair of CPD by UV1C were compared for parallel G-quadruplex-rich and hybrid G-quadruplex-rich samples. Spectral variations were indicative of structural differences in parallel and hybrid G-quadruplexes before and after CPD cleavage. Differences were also observed when compared to the CPD repair spectrum by CPD photolyase. The spectral differences during CPD repair by either protein or DNAzyme suggest the local environment of the substrates, the surrounding protein, or the aqueous solution.
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Affiliation(s)
- Tatsuya Iwata
- Department
of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Yuhi Kurahashi
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - I Made Mahaputra Wijaya
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department
of Life Science and Applied Chemistry, Nagoya
Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
- OptoBioTechnology
Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Taylor A, Heyes DJ, Scrutton NS. Catalysis by Nature's photoenzymes. Curr Opin Struct Biol 2022; 77:102491. [PMID: 36323132 DOI: 10.1016/j.sbi.2022.102491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/22/2022] [Accepted: 10/01/2022] [Indexed: 12/14/2022]
Abstract
Photoenzymes use light to initiate biochemical reactions. Although rarely found in nature, their study has advanced understanding of how light energy can be harnessed to facilitate enzyme catalysis, which is also of importance to the design and engineering of man-made photocatalysts. Natural photoenzymes can be assigned to one of two families, based broadly on the nature of the light-sensing chromophores used, those being chlorophyll-like tetrapyrroles or flavins. In all cases, light absorption leads to excited state electron transfer, which in turn initiates photocatalysis. Reviewed here are recent findings relating to the structures and mechanisms of known photoenzymes. We highlight recent advances that have deepened understanding of mechanisms in biological photocatalysis.
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Affiliation(s)
- Aoife Taylor
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, M1 7DN, United Kingdom
| | - Derren J Heyes
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, M1 7DN, United Kingdom. https://twitter.com/DerrenHeyes
| | - Nigel S Scrutton
- Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, M1 7DN, United Kingdom.
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